rs4859259

Positions:

• chr3-182946759-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020640.4(DCUN1D1):​c.700+479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,818 control chromosomes in the GnomAD database, including 28,577 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (28577 hom., cov: 30)
• Consequence: DCUN1D1 NM_020640.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

Genes affected

DCUN1D1 (HGNC:18184): (defective in cullin neddylation 1 domain containing 1) Enables cullin family protein binding activity. Involved in positive regulation of protein neddylation and regulation of protein ubiquitination. Located in cytosol and nucleoplasm. Part of ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCUN1D1	NM_020640.4	c.700+479C>T		intron_variant		ENST00000292782.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCUN1D1	ENST00000292782.9	c.700+479C>T		intron_variant		1	NM_020640.4	P1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83478 AN: 151700 Hom.: 28591 Cov.: 30

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.566

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.550 AC: 83438 AN: 151818 Hom.: 28577 Cov.: 30 AF XY: 0.547 AC XY: 40574 AN XY: 74234

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.560

Alfa AF: 0.714 Hom.: 93137

Bravo AF: 0.521

Asia WGS AF: 0.375 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4859259; hg19: chr3-182664547;